Chromatin assembly factor 1 suppresses epigenetic reprogramming toward adaptive drug resistance

The long-term effectiveness of targeted cancer therapies is limited by the development of resistance.Although epigenetic reprogramming has been implicated in resistance,the mechanisms remain elusive.Herein,we demonstrate that increased chromatin accessibility is involved in adaptive BRAF inhibitor(BRAFi)-resistance in melanoma cells.We observed loss of chromatin assembly factor 1(CAF-1)and its related histone H3 lysine 9 trimethylation(H3K9me3)with adaptive BRAFi resistance.We further showed that depletion of CAF-1 provides chromatin plasticity for effective reprogramming by AP1 components to promote BRAFi resistance.Our data sug-gest that therapeutic approaches to restore H3K9me3 levels may compensate for the loss of CAF-1 and,in turn,suppress resistance to BRAF inhibitors.

The thylakoid membrane protein NTA1 is an assembly factor of the cytochrome b6f complex essential for chloroplast development in Arabidopsis

The cytochrome b_(6f)(Cyt b_(6f))complex is a multisubunit protein complex in chloroplast thylakoid membranes required for photosynthetic electron transport.Here we report the isolation and characterization of the new tiny albino 1(nta1)mutant in Arabidopsis,which has severe defects in Cyt b_(6f) accumulation and chloroplast development.Gene cloning revealed that the nta1 phenotype was caused by disruption of a single nuclear gene,NTA1,which encodes an integral thylakoid membrane protein conserved across green algae and plants.Overexpression of NTA1 completely rescued the nta1 phenotype,and knockout of NTA1 in wild-type plants recapitulated the mutant phenotype.Loss of NTA1 function severely impaired the accumulation of multiprotein complexes related to photosynthesis in thylakoid membranes,particularly the components of Cyt b_(6f).NTA1 was shown to directly interact with four subunits(Cyt b6/PetB,PetD,PetG,and PetN)of Cyt b_(6f) through the DUF1279 domain and C-terminal sequence to mediate their assembly.Taken together,our results identify NTA1 as a new and key regulator of chloroplast development that plays essential roles in assembly of the Cyt b_(6f) complex by interacting with multiple Cyt b_(6f) subunits.

A novel protein domain is important for photosystem Ⅱ complex assembly and photoautotrophic growth in angiosperms

Photosystem Ⅱ(PSⅡ)is a multi-subunit protein complex of the photosynthetic electron transport chain that is vital to photosynthesis.Although the structure,composition,and function of PSⅡ have been extensively studied,its biogenesis mechanism remains less understood.Thylakoid rhodanese-like(TROL)provides an anchor for leaf-type ferredoxin:NADP^(+)oxidoreductase.Here,we report the chacterizaton of a second type of TROL protein,TROL2,encoded by seed plant genomes whose function has not previously been reported.We show that TROL2 is a PSⅡ assembly cofactor with essential roles in the establishment of photoautotrophy.TROL2 contains a 45-amino-acid domain,termed the chlorotic lethal seedling(CLS)domain,that is both necessary and sufficient for TROL2 function in PSⅡ assembly and photoautotrophic growth.Phylogenetic analyses suggest that TROL2 may have arisen from ancestral TROL1 via gene duplication before the emergence of seed plants and acquired the CLS domain via evolution of the sequence encoding its N-terminal portion.We further reveal that TROL2(or CLS)forms an assembly cofactor complex with the intrinsic thylakoid membrane protein LOW PSⅡ ACCUMULATION2 and interacts with small PSⅡ subunits to facilitate PSⅡ complex assembly.Collectively,our study not only shows that TROL2(CLS)is essential for photoautotrophy in angiosperms but also reveals its mechanistic role in PSⅡ complex assembly,shedding light on the molecular and evolutionary mechanisms of photosynthetic complex assemblyin angiosperms.

Structural insights into the functions of Raf1 and Bsd2 in hexadecameric Rubisco assembly

Hexadecameric formI Rubisco,which consisting consists of eight large(RbcL)and eight small(RbcS)subunits,is the most abundant enzyme on earth.Extensive efforts to engineer an improved Rubisco to speed up its catalytic efficiency and ultimately increase agricultural productivity.However,difficulties with correct folding and assembly in foreign hosts or in vitro have hampered the genetic manipulation of hexadecameric Rubisco.In this study,we reconstituted Synechococcus sp.Pcc6301 Rubisco in vitro using the chaperonin system and assembly factors from cyanobacteria and Arabidopsis thaliana(At).Rubisco holoenzyme was produced in the presence of cyanobacterial Rubisco accumulation factor 1(Raf1)alone or both AtRaf1 and bundle-sheath defective-2(AtBsd2)from Arabidopsis.RbcL released from GroEL is assembly capable in the presence of ATP,and AtBsd2 functions downstream of AtRaf1.Cryo-EM structures of RbcL8-AtRaf18,RbcL8-AtRaf14-AtBsd2s,and RbcLs revealed that the interactions between RbcL and AtRaf1 are looser than those between prokaryotic RbcL and Raf1,with AtRaf1 tilting 7°farther away from RbcL.AtBsd2 stabilizes the flexible regions of RbcL,including the N and C termini,the 60s loop,and loop 6.Using these data,combined with previous findings,we propose the possible biogenesis pathways of prokaryotic and eukaryotic Rubisco.

The Cyclophilin AtCYP71 Interacts with CAF-1 and LHP1 and Functions in Multiple Chromatin Remodeling Processes

Chromatin is the primary carrier of epigenetic information in higher eukaryotes. AtCYP71 contains both cyclophilin domain and WD40 repeats. Loss of AtCYP71 function causes drastic pleiotropic phenotypic defects. Here, we show that AtCYP71 physically interacts with FAS1 and LHP1, respectively, to modulate their distribution on chromatin. The Ihpl cyp71 double mutant showed more severe phenotypes than the single mutants, suggesting that AtCYP71 and LHP1 synergistically control plant development. Such synergism was in part illustrated by the observation that LHP1 association with its specific target loci requires AtCYP71 function. We also demonstrate that AtCYP71 physically interacts with FAS1 and is indispensable for FAS1 targeting to the KNAT1 locus. Together, our data suggest that AtCYP71 is involved in fundamental processes of chromatin assembly and histone modification in plants.

SNOWY COTYLEDON 2 Promotes Chloroplast Development and Has a Role in Leaf Variegation in Both Lotus japonicus and Arabidopsis thaliana

Plants contain various factors that transiently interact with subunits or intermediates of the thylakoid multiprotein complexes, promoting their stable association and integration. Hence, assembly factors are essential for chloroplast development and the transition from heterotrophic to phototrophic growth. Snowy cotyledon 2 （SCO2） is a DNAJ-like protein involved in thylakoid membrane biogenesis and interacts with the light-harvesting chlorophyll-binding protein LHCBI. In Arabidopsis thaliana, SCO2 function was previ- ously reported to be restricted to cotyledons. Here we show that disruption of SC02 in Lotus japonicus results not only in paler cotyledons but also in variegated true leaves. Furthermore, smaller and pale- green true leaves can also be observed in A. thaliana sco2 （atsco2） mutants under short-day conditions. In both species, SCO2 is required for proper accumulation of PSlI-LHCll complexes. In contrast to other variegated mutants, inhibition of chloroplastic translation strongly affects L. japonicus sco2 mutant devel- opment and fails to suppress their variegated phenotype. Moreover, inactivation of the suppressor of variegation AtClpR1 in the atsco2 background results in an additive double-mutant phenotype with variegated true leaves. Taken together, our results indicate that SCO2 plays a distinct role in PSll assembly or repair and constitutes a novel factor involved in leaf variegation.

An MCIA-like complex is required for mitochondrial complex Ⅰ assembly and seed development in maize

During adaptive radiation,mitochondria have co-evolved with their hosts,leading to gain or loss of subunits and assembly factors of respiratory complexes.Plant mitochondrial complex Ⅰ harbors40 nuclearand 9 mitochondrial-encoded subunits,and is formed by stepwise assembly during which different intermediates are integrated via various assembly factors.In mammals,the mitochondrial complex Ⅰ intermediate assembly(MCIA)complex is required for building the membrane arm module.However,plants have lost almost all of the MCIA complex components,giving rise to the hypothesis that plants follow an ancestral pathway to assemble the membrane arm subunits.Here,we characterize a maize crumpled seed mutant,crk1,and reveal by map-based cloning that CRK1 encodes an ortholog of human complex Ⅰ assembly factor 1,zNDUFAF1,the only evolutionarily conserved MCIA subunit in plants.zNDUFAF1 is localized in the mitochondria and accumulates in two intermediate complexes that contain complex Ⅰ membrane arm subunits.Disruption of zNDUFAF1 results in severe defects in complex Ⅰ assembly and activity,a cellular bioenergetic shift to aerobic glycolysis,and mitochondrial vacuolation.Moreover,we found that zNDUFAF1,the putative mitochondrial import inner membrane translocase ZmTIM17-1,and the isovaleryl-coenzyme A dehydrogenase ZmIVD1 interact each other,and could be co-precipitated from the mitochondria and co-migrate in the same assembly intermediates.Knockout of either ZmTIM17-1 or ZmIVD1 could lead to the significantly reduced complex Ⅰ stability and activity as well as defective seeds.These results suggest that zNDUFAF1,ZmTIM17-1 and ZmIVD1 probably form an MCIA-like complex that is essential for the biogenesis of mitochondrial complex Ⅰ and seed development in maize.Our findings also imply that plants and mammals recruit MCIA subunits independently for mitochondrial complex Ⅰ assembly,highlighting the importance of parallel evolution in mitochondria adaptation to their hosts.